## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-worknov/Alignment/2024-08-28_Rogachev/G2073_21/G2073_21_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-worknov/Alignment/2024-08-28_Rogachev/G2073_21/G2073_21_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-worknov/Alignment/2024-08-28_Rogachev/G2073_21/G2073_21_dedup_metrics.txt CREATE_INDEX=true    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false FLOW_MODE=false FLOW_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Mon Dec 01 10:32:13 NOVT 2025

## METRICS CLASS	picard.sam.DuplicationMetrics
LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
Unknown Library	39617	139554907	118652811	51479	8536	8512898	0	0.061022	1096878857

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	123095511	123095511
2.0	1.880532	7436027	7436027
3.0	2.655868	470014	470014
4.0	3.338577	33953	33953
5.0	3.939724	3944	3944
6.0	4.469052	1156	1156
7.0	4.935143	523	523
8.0	5.345551	305	305
9.0	5.706928	142	142
10.0	6.025133	102	102
11.0	6.305322	56	56
12.0	6.552037	53	53
13.0	6.769278	28	28
14.0	6.960565	25	25
15.0	7.129	16	16
16.0	7.277312	12	12
17.0	7.407905	9	9
18.0	7.522897	17	17
19.0	7.624151	11	11
20.0	7.713308	8	8
21.0	7.791814	12	12
22.0	7.860941	6	6
23.0	7.92181	4	4
24.0	7.975406	7	7
25.0	8.0226	3	3
26.0	8.064155	5	5
27.0	8.100746	3	3
28.0	8.132966	2	2
29.0	8.161336	10	10
30.0	8.186317	4	4
31.0	8.208313	8	8
32.0	8.227682	2	2
33.0	8.244736	2	2
34.0	8.259754	3	3
35.0	8.272977	3	3
36.0	8.28462	1	1
37.0	8.294872	0	0
38.0	8.3039	1	1
39.0	8.311849	0	0
40.0	8.318848	1	1
41.0	8.325012	1	1
42.0	8.330438	1	1
43.0	8.335217	1	1
44.0	8.339425	0	0
45.0	8.34313	1	1
46.0	8.346392	0	0
47.0	8.349265	2	2
48.0	8.351794	1	1
49.0	8.354021	2	2
50.0	8.355982	2	2
51.0	8.357709	0	0
52.0	8.35923	1	1
53.0	8.360569	3	3
54.0	8.361748	0	0
55.0	8.362786	1	1
56.0	8.3637	0	0
57.0	8.364505	1	1
58.0	8.365213	1	1
59.0	8.365837	0	0
60.0	8.366387	0	0
61.0	8.366871	0	0
62.0	8.367297	0	0
63.0	8.367672	0	0
64.0	8.368002	0	0
65.0	8.368293	0	0
66.0	8.368549	0	0
67.0	8.368775	0	0
68.0	8.368973	0	0
69.0	8.369148	0	0
70.0	8.369302	0	0
71.0	8.369438	0	0
72.0	8.369557	0	0
73.0	8.369662	0	0
74.0	8.369755	0	0
75.0	8.369836	0	0
76.0	8.369908	0	0
77.0	8.369971	0	0
78.0	8.370027	0	0
79.0	8.370076	0	0
80.0	8.370119	0	0
81.0	8.370157	0	0
82.0	8.37019	0	0
83.0	8.37022	0	0
84.0	8.370246	0	0
85.0	8.370269	0	0
86.0	8.370289	0	0
87.0	8.370306	0	0
88.0	8.370322	0	0
89.0	8.370336	0	0
90.0	8.370348	0	0
91.0	8.370358	0	0
92.0	8.370368	0	0
93.0	8.370376	0	0
94.0	8.370383	0	0
95.0	8.37039	0	0
96.0	8.370395	0	0
97.0	8.3704	0	0
98.0	8.370405	0	0
99.0	8.370408	0	0
100.0	8.370412	0	0
102.0	0	1	1
118.0	0	1	1